Equestrian Cataclysm
by Foxchild11
Summary: Everything seems quite regular in Ponyville. Until the darkness comes and everything deemed evil by Ponykind returns. It's up to Twilight and her friends to find out what's going on, and why. Warning: This has some graphic scenes, so if you don't want to see ponies murdered I wouldn't read this fic.
1. Chapter 1

_Hello! Just a quick word from me :) This is my first story, and I'm including several OC's from my friends. But mostly the story consists of the mane six or villains or other known ponies from the show. Please don't hate :( I will take constructive criticism though, I love that. It makes everything better XD Anyways enjoy the story!_

**_NOTE: I do NOT own anything except the OCs. All things related to the MLP:FiM is property of Lauren Faust and Hasbro._**

Chapter 1

Basement

Everything was a fairly regular day in Ponyville, just as you would imagine it. AJ selling things at a stand, Rarity delivering an order, Pinkie eating some cake at sugarcube corner. Just imagine not a cloud in the sky- Rainbow Dash's doing- and Fluttershy guiding some ducks back to their nest. It was simply perfect; Well it all went downhill from there.

"Twilight, please. You've studied enough!" Spike pestered. They were sitting at the cafe next to the "Sophas & Quills" shop.

"Spike, please. This is extremely important- I'm working on my new 'Equestrian History' section. Which is more important than nearly anything- Since I'm taking on the role of princess, I have to have prime knowledge of all of this!"

"Okay, okay. All I needed was a simple 'yes' or 'no'." Spike leaned back in his chair with a sigh. About to close his eyes, he saw in the distance something like a meteorite. But it was a glowing green color. His eyes shot open in amusement.

"T-T-Twi..." he stuttered, seeing as it was getting closer. She rolled her eyes and looked up from her book titled "Bygone Equestria". She followed Spike's finger to the glowing green object. Her eyes widened, fascinated. But as she saw it was just seconds away, she snapped out of the trance. Hopping out of her chair, she ran towards all the other ponies.

"Everypony! Run! Run! Get in your basements!" She observed very little in her split second of time to get up, but everything she saw stuck. Crying children, Fluttershy's wing closing shut, making her fall to the ground. Ponies of all colors, races, and sizes bolting for cover. The sky darkened, going black and the small amount of light that there was highlighted the clouds. More green objects became visible through the grey, beige colored clouds, only making everypony panic more.

Twilight used her magic to pick up Spike as they ran to take cover at Sugarcube Corner. She knew it had a basement, which would be the safest place for everypony. Bolting to the entrance, she stopped and turned to the chaotic town's square. "Everypony! In here! It'll be safe!" A stampede of about seven ponies shoved into the sweets shop, adding to the stressed Mr. and Mrs. Cake and their crying children. Twilight soon followed, hearing the worried sounds of all of the ponies.

Everypony, please calm down. Make your way into the basement." The pony's murmurs quieted down with Twilight's reassurance. Spike hopped down and followed all of the others. She turned and looked out the door to see Changelings catapulting towards Ponyville. "T-t-they're back?!" Her face turned from calm and collected to worried and chaotic, reflecting the rest of the environment. She looked at all the ponies shuffling into the basement, realising that any one of them could be fakes.

Finally closing the door and following through into the basement, she lit a candle (a few, for that matter) then closed the door, not needing the light anymore. She sighed, then turned to see who was there.

Spike was there, of course. Then there was Mr. and Mrs. Cake, and their two children. That made five. Then, there was Lyra, Ms. Cherilee, Carrot Top, Featherlane, Octavia, Vinyl, and... Fluttershy! Twilight didn't see her come in, but it was good to have a friend in there.

"Fluttershy!" Twilight shoved through the crowd to greet her.

"Hi Twilight" Fluttershy stated in her trademark shy, high-pitched voice.

"Oh my, Fluttershy! What happened to your wing?" Twi said, worried.

"Oh, well... I hurt it when I fell" she said, blushing, embarrassed.

"Here, let me find something for you. That needs to be patched up!" Twilight saw a shelf near the back with a few boxes, helping herself to it's contents. Opening a few, most of them held sprinkles and fondant. Which wasn't a surprise, since these boxes did belong to the Cakes. Digging in a few more, she found a plastic box on the inside of one of the cardboard ones. By dumb luck, it happened to have a big red plus on it. "Perfect!" Twilight exclaimed. She pulled it out and opened it to find that it had everything. Medicine, band-aids, and...bandages! She pulled them out and trotted back over to Fluttershy.

"Here. Some bandages should help with hurting it more." She unrolled the cloth then re-wrapped it around Fluttershy's torso, letting her broken wing get wrapped and leaving her other one open to breathe. Twilight stepped back and smiled. Fluttershy then returned the gesture, turning and walking off.

Twilight made the decision to go outside just to check if anything got worse. Then, she assumed that it would be the right thing to do to go check and see that all the other ponies were safe. "Spike?" Twilight spoke out into the basement. He pushed his way up to the front, meeting Twilight. "Yeah Twi?" "Spike, I need you to remember that invisibility spell." "Oh, sure twi". Spike recited the instructions, and as he did so Twilight tried it out. After a pink burst from her horn, there was nothing. "Did it work?" "Good job twilight! What did you need it for anyways?" "Spike, I'm sorry. I can't tell you- But I need you to keep an eye on everybody here, alright?" "Um, sure... But be careful, ok?" Twilight smiled, knowing that Spike couldn't see, then responded, "I will."

She bolted out the door from the basement, then out of the colorful one near the front. Looking out on ponyville, her heart sank. The buildings were torn up, some carts were on fire, and there wasn't any pony outside. There were changelings marauding through the streets, and the sky was black as night. "But... It was the middle of the day when we went into the basement!" She looked up to see a large blue mist in the air... "Nightmare Moon!"

Not only were the changelings back, but nightmare moon too? But if that's nightmare moon, then it also must be luna! Why would she do this? She was perfectly fine and respected! Twilight didn't understand any of this. Then, out of nowhere, a pink cloud hurricane breezed into view with brown droplets pouring down where there should be rain. "No... Him too? What is this? Some kind of ponyclypse? It couldn't have been possible. All these people were gone for good! She darted to the library to see if she could gather information, along the way checking inside the houses. She didn't see anybody, which could be good or bad.

She approached the library and opened the door, to find that all her other friends had gathered. Sorrow painted onto their faces, looking down at the ground. Twilight knew that the spell would wear off soon, but she needed to not alarm them. They were in a circle around a part of the library. Twilight, remembering her wings and knowing she knew how to control them, flew up over the ponies. Looking down, she let out a gasp as a tear trickled down her face.

"G-G-G-Girls?" she sobbed. Looking down, she sobbed as she saw the torn up, burnt bodies of the Crusaders. Bows torn, manes burnt, bloody hides ratted with dirt and holes. Twilight dropped to the ground and began to sob even harder. The invisible spell died off, leaving her visible to her friends. This was not right. Fillies being murdered? What else could happen? This was war.

Twilight's face went serious as she wiped the tears from her face. She turned to see the four unaware ponies. "Girls, this is war. Things like this cannot happen. It's mutiny, disharmony... We need to stop this." The four turned to face her, following the same actions of wiping their tears and letting their face turn serious. They nodded in agreement. "Where's fluttershy?" Rainbow Dash asked. "In the basement at sugarcube corner. Along with eleven others." Pinkie nodded and walked to the big horse statue in the center of the library. She pressed it's eye, and the horses jaw dropped open to form a secret entrance. "Pinkie... What is this?!" Rarity questioned, her mascara dripping and hair very ratted and un neat. "I have hidden passages all over ponyville that lead to Sugarcube Corner. In case of an emergency," she replied in her famous Pinkie-Pie tone. They filed in through the wooden horse mouth, into a dark torch-lit passage with many other paths. They followed down until they saw a staircase and walked up to it's entrance. They opened the trap door to find that they were behind the counter at Sugarcube. They all walked around to the basement door and walked down the short amount of steps. Twilight lit her horn for light, and in dismay her face dropped to sorrowful once more.

Dead. All the ponies that were down there were dead! Vinyl, Carrot top, Mr. and Mrs. cake, their children... Fluttershy stood, blood-caked and alive behind all the dead bodies. An evil grin on her face. "Well hello, dear" she said in an extremely familiar tone. A flash of green, so blinding that the others had to cover their eyes, emitted from the false Fluttershy. When they looked back, they saw a sight they never wanted to see again.

Chrysalis.


	2. Chapter 2

Chapter 2

"What are you doing here, you filthy bug!" Rainbow Dash spat at Chrysalis.

"Mm, well I wouldn't speak to me THAT way, now would we?" she said back in her voice, similar to that of a snake's. She let the glow of her twisted, dark horn light a darkened corner of the basement. When the darkness cleared, the five ponies choked.

There in the shadows, a poor helpless Fluttershy tied up and bleeding. A white, dirty cloth silenced her screams as she tried to get past the cloth to wail. Tears streamed down her coat, burning the cuts matting her yellow hide. Every time the salty sorrow grazed past the fleshy, burnt marks of Chrysalis' horn, Fluttershy squirmed in pain, forcing her to hurt even more. She was held up by bare chains, no hoof-cuffs, just metal chinks digging into her wrists causing red burn marks to form. Who would do this to such a sweet, shy, innocent pony?

"Let her go you! Or I'll... I'll..." Applejack threatened. "Or you'll what?" Chrysalis spat back. She turned at her with a hiss, then aiming her horn at the five ponies' hooves bolted a green strike, forcing them to stay put with the green slime holding them down. "Let us go you horrid creature, with absolutely NO sense in hygiene Or style! Just look at your hooves! And those WINGS!" Rarity teased, trying to aggravate her. Chrysalis only giggled.

"Oh, **I **have no style?" Rarity blinked but when she opened her lovely lashed eyes, she saw herself. But... It wasn't her. Rarity's hair was a horrid green mess, her hooves mimicking Chrysalis'. She had her wings as well. Rarity screamed, trying to move but unable to because of the goo.

"Agh! You horrid HORRID thing!"

"Well, it teaches you now doesn't it?" Chrysalis went back to her regular insect-like form and walked back near the wall, stepping over the bodies and pools of blood. "Now that I'm back, I guess I'll go FEED now. Goodbye, dears!"

Chrysalis shoved past the five and opened the basement door, letting in the sounds of screaming, panicking ponies. Twilight looked around, then realised that she was magic. She pointed her horn down at the green goo and zapped it, making it melt. She smiled. Stepping back she did the same to her friends, then turned to look at fluttershy. She once again pointed her horn, then zapped at the chains making fluttershy fall to the ground. She made a small whimper as she fell then gathered herself. She attempted to stand but fell to the ground, to weakened and in pain. "Who would do such a thing to you, Fluttershy?" Twilight took out the cloth in her mouth and threw it to the ground. She sat beside her and comforted her, wrapping her wing around her. "It's all going to be okay."

Twilight stood and faced Rainbow Dash, Pinkie Pie, Rarity, and Applejack. "We need to get to the hospital. I'm sure that there are some others there- That's where a resistance would be. Plus, Fluttershy needs to see a doctor. It looks like her front hooves are broken, and she has so many cuts..." She saw all the others nod. "Anything for Fluttershy," Pinkie agreed. All the others nodded. "Let's gather what we can from down here to bring in case there's not much at the hospital." Applejack suggested. They spread out, avoiding the gory scene on the cement floor of the basement and looking through boxes on the walls and all the other compartments. Pinkie stayed still, a sad look on her face as she glanced around. She walked around the blood and ponies to the corner where Fluttershy sat, alone and sobbing. She sat by her and looked into her eyes, smiling. They comforted each other as the others looked around the basement.

"Look what I found!" Rarity exclaimed, raising up ten saddlebags for them. The four smiled and came to grab them, latching them around their saddles. They were hemp with worn out buttons, but it was better than nothing. Rainbow dash found a sack of apples and threw them into the bag. Twilight took the first-aid she had used for Fluttershy and stuck it in her left bag. Applejack found a camping kit with all sorts of things- Knives, blankets, ect.- Everything they needed. Rarity looked around and found some crackers and bread, along with some well-sealed milk near the very back. The girls were satisfied with their finds, and went back to gather Pinkie and Fluttershy.

As Fluttershy attempted to rise, Pinkie stopped her and helped her up, putting their arms around each other and walking in sync. They stayed like that the entire time.

The six ponies flew, hunched, and trotted up the stairs. When they opened the door out of the basement, they laid their eyes upon a horrid sight. The entire roof of Sugarcube Corner was blasted off, leaving the blackened sky beaming down on the small herd. "Run!" Twilight urged. She bolted to where the door would be and leapt through it, having Rarity, Applejack, and Rainbow Dash follow. But, a pained Fluttershy was hunched around Pinkie, making them both slow as could be.

Twilight turned and saw in distress the two slowed ponies. They couldn't take the passage, as it was heading in the wrong direction. Suddenly, an idea sparked in Twilight's mind. "Pinkie, Fluttershy, stay put. I have an idea. The rest of you, head towards the hospital. We'll meet you there." The sounds of war raged above them- Flames, crashing, rain, explosions. Twilight took a strong stance and bent her head down, charging up her horn. She aimed at Pinkie and blasted a cloud-walking spell from when they went to cloudsdale with Rainbow Dash. Then, she started to aim a little higher up and formed a puff of steam which then became a cloud. "Get on- I'll get you to the hospital." Pinkie got on first, and the cloud lowered on que. Fluttershy weakly walked onto it then laid herself down. Pinkie then went back to cuddling her, making her feel safe. They both covered their ears as Twilight used magic to guide the cloud out the door.

Upon leaving the door's vicinity, Twilight bolted out towards the hospital, heading northwest. The rain beat down on their heads, blocking out every other sound. Out of nowhere, large black crystals began to shove up through the earth, making it difficult for Twilight to maneuver the cloud carrying precious cargo. After a good minute of dodging the large opaque black rocks, she took a moment to realise that it was Sombra. "Sombra! You bastard!" Twilight screamed out at him. She heard the sound of his laughter as she galloped faster. The hospital came into view, but there were barrels and planks blocking the door. She ran to the bolted up entrance and started to bang on it. "It's me! Twilight! Let me in, please! I have a hurt Pegasi with me!" She moved out all the barrels and continued rapping on the door. She heard it unlock, then a large blast cleared the wood and knocked the door wide open. Twilight ran in, panting, then turned to again bolt the door shut.

After having help from somepony, she sat against the wall and breathed hard in relief. She turned to see who had helped, but she couldn't tell who. There was a black hood covering her face. "Thank... You... For... Helping... Us..." Twilight panted. The hooded figure stood on both hind legs and rose on her staff, then uncloaked her face to reveal a lovely pegasi with a striped mane and bangs. "No problem." she smiled. "What's your name?" Twilight questioned. The unknown pegasi opened her mouth to speak, but was interrupted by a green and purple dash shoving her to the side.

"TWILY!" Spike screamed, overjoyed to see his friend. "Spike! I was afraid I'd lost you..." They hugged each other, sitting like that for a while. She pulled back and smiled. Then remembering Fluttershy and pinkie, Twilight's eyes widened as she turned to look at the cloud. It was too high for her to see, so she lowered it. When she did, there on the cloud was an even more hurt Fluttershy. One of Sombra's crystals had stabbed through her wing, letting blood seep into the cloud, staining it. A tear trickled down Twilight's face. "She's just unconscious. We have to help her." Pinkie spoke, helpfully. Twilight nodded and turned to spike. "I need you to take them to the emergency wing. Hurry, please." Twilight cast a "Follow" spell on the cloud, making it follow where Spike went. He nodded then ran off, leaving her alone. She looked around at the refuge, seeing all the distress that was rattling Equestria. Lots of panicked ponies, mothers sitting with their frightened fillys. Twilight was sad- This place was so awful. She sat on her rump and sighed. Then, she remembered the mysterious pony that had opened the door. She looked around the lobby of the hospital, and found her bandaging a hurt Peppermint Twist. Twilight trotted over to find out who she was. "Um, Hello. I'm Twilight Sparkle." The mysterious pony turned and stood, like before, being held up by a lovely staff.

"Hello. My name is Elequine Moondark." she responded. Twilight smiled.

"Thank you elequine, for helping me inside. I fear that this is going to get much much worse, and getting calm ponies that are willing to help is very important."

Elequine smiled back."No problem. I'm leader here at this refuge, and so I have to help the ponies that need me."

"Wow, so you started this hospital base camp?" Twilight was impressed. She had never seen this pegasi around but she knew that she would be good.

"Sure did. I saw all of this before it was coming, so I prepared us for a month of food and stuff." Suddenly Twilight had an idea.

"Elequine, I need to get to Canterlot to see the princes, but obviously I can't do it alone. I'm forming a group to get there, and I was thinking of starting another base camp in Canterlot. With my brother, Shining Armor, and his protection spell, we'll be safe enough to transport ponies there. It's the best thing we can do for now. Do you think you and I could round up as many ponies as possible to get to Canterlot? Ponyville isn't safe. They need to get out of here."

"Of course I will, twilight. Holo on- I'll get you two of my best ponies to go with you. You can take them to round up all the others. Bring them back here, then we can take them to the train. Deal?"

"Deal."

Elequine walked off, and a minute later brought back two ponies. A mare and a stallion. "This is Lacey. She's an extremely talented pony, and can fly very well. She'll be good at getting the ponies together."  
"Oh, stop it El! I'm not the greatest." She blushed. She then pointed to the stallion. He had green hair and a sleek grey coat. "This is . He's a very who she was.

"Hello, I'm Twilight Sparkle." she told her. The pony turned from Twist and walked to Twilight. Uncloaking herself, she had revealed lovely purple eyes and a striped mane. Her pegasi wings folded at her side neatly, the feathers being slightly pulled down. She stood on her hind legs powerful unicorn so you can for sure use him." "Of course you can. Anything you need, I can do it." The stallion smiled. "We better go round up all the ponies. I'll meet you back here in thirty minutes." Twilight started to open up the door, taking down the planks


End file.
